phenix.protocols.protocol_real_space_refine module

class phenix.protocols.protocol_real_space_refine.PhenixProtRunRSRefine(**kwargs)

Bases: phenix.protocols.protocol_refinement_base.PhenixProtRunRefinementBase

Tool for extensive real-space refinement of an atomic structure against the map provided. The map can be derived from X-ray or neutron crystallography, or cryoEM. The program obtains a model that fits the map as well as possible having appropriate geometry. The model should not show validation outliers, such as Ramachandran plot or rotamer outliers.

REALSPACEFILE = 'real_space.mrc'

VALIDATIONCRYOEMPKLFILE = 'validation_cryoem.pkl'

createOutputStep()

runMolprobityStep(tmpMapFile)

runRSrefineStep(tmpMapFile)

runValidationCryoEMStep(tmpMapFile)